setwd(“X:/PATH/TO/YOUR/FILE/")
table <- as.matrix(read.csv("./dataExample_gcba815_100.csv", header=TRUE, row.names=1))
class(table) <- “numeric”
s1 <- subset(table, select="sample_1")
s2 <- subset(table, select="sample_2") 
pdf("Comparison_S1S2_scatter.pdf")

#### Version 1 ####
# plot(s1, s2)
###################

#### Version 2 ####
# plot(log10(s1+1), log10(s2+1))
###################

#### Version 3 ####
# plot(log10(s1+1), log10(s2+1), xlab="sample 1 (log10 transformed)", ylab="sample 2 (log10 transformed)", pch=19)
###################

#### Version 4 ####
# plot(log10(s1+1), log10(s2+1), xlab="sample 1 (log10 transformed)", ylab="sample 2 (log10 transformed)", pch=19, xaxs="i", yaxs="i")
###################

#### Version 5 ####
# plot(log10(s1+1), log10(s2+1), xlab="sample 1 (log10 transformed)", ylab="sample 2 (log10 transformed)", pch=19, xaxs="i", yaxs="i", xlim=c(0, 2), ylim=c(0,2))
###################

#### Version 6 ####
# cor(log10(s1+1),log10(s2+1))
# plot(log10(s1+1), log10(s2+1), xlab="sample 1 (log10 transformed)", ylab="sample 2 (log10 transformed)", pch=19, xaxs="i", yaxs="i", xlim=c(0, 2), ylim=c(0,2), main=paste(c("r = ", round(cor(log10(s1+1), log10(s2+1)), digits=3)), collapse=""))
###################

## Final Version ##
# plot(log10(s1+1), log10(s2+1), xlab="sample 1 (log10 transformed)", ylab="sample 2 (log10 transformed)", pch=19, xaxs="i", yaxs="i", xlim=c(0, 2), ylim=c(0,2), main=paste(c("r = ", round(cor(log10(s1+1), log10(s2+1)), digits=3)), collapse=""))
# abline(lm(log10(s1+1)~log10(s2+1)), col="red")
# abline(a=0, b=1, col="blue")
###################

dev.off()